#13948 sample & test form changes

sormas-api/src/main/java/de/symeda/sormas/api/feature/FeatureConfigurationFacade.java

@@ -55,6 +55,12 @@ Page<FeatureConfigurationIndexDto> getIndexPage(
 
 	void saveFeatureConfiguration(@Valid FeatureConfigurationIndexDto configuration, FeatureType featureType);
 
+	/**
+	 * Enables or disables a server-level feature (one with no region/district/disease scope), seeding the
+	 * configuration row if it does not exist yet. Intended for the administrator feature-configuration view.
+	 */
+	void setServerFeatureEnabled(FeatureType featureType, boolean enabled);
+
 	void deleteAllFeatureConfigurations(FeatureConfigurationCriteria criteria);
 
 	void deleteAllExpiredFeatureConfigurations(Date date);

sormas-api/src/main/java/de/symeda/sormas/api/feature/FeatureType.java

@@ -14,9 +14,18 @@
  */
 package de.symeda.sormas.api.feature;
 
-import static de.symeda.sormas.api.common.DeletableEntityType.*;
+import static de.symeda.sormas.api.common.DeletableEntityType.CASE;
+import static de.symeda.sormas.api.common.DeletableEntityType.CONTACT;
+import static de.symeda.sormas.api.common.DeletableEntityType.EVENT;
+import static de.symeda.sormas.api.common.DeletableEntityType.EVENT_PARTICIPANT;
+import static de.symeda.sormas.api.common.DeletableEntityType.IMMUNIZATION;
+import static de.symeda.sormas.api.common.DeletableEntityType.TRAVEL_ENTRY;
 
-import java.util.*;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
 
 import com.google.common.collect.ImmutableMap;
 
@@ -57,6 +66,18 @@ public enum FeatureType {
 			SAMPLES_LAB },
 		null,
 		null),
+	SAMPLE_ADD_PATHOGEN_TEST(true,
+		true,
+		new FeatureType[] {
+			SAMPLES_LAB },
+		null,
+		null),
+	PATHOGEN_TEST_RESULT_REQUIRED(true,
+		true,
+		new FeatureType[] {
+			SAMPLES_LAB },
+		null,
+		null),
 	TASK_MANAGEMENT(true, true, null, null, ImmutableMap.of(FeatureTypeProperty.ALLOW_FREE_EDITING, Boolean.FALSE)),
 	WEEKLY_REPORTING(true, true, null, null, null),
 	IMMUNIZATION_MANAGEMENT(true, true, null, null, ImmutableMap.of(FeatureTypeProperty.REDUCED, Boolean.FALSE)),

sormas-api/src/main/java/de/symeda/sormas/api/i18n/Captions.java

@@ -2078,6 +2078,7 @@ public interface Captions {
 	String facilityArchivedFacilities = "facilityArchivedFacilities";
 	String facilityType = "facilityType";
 	String facilityTypeGroup = "facilityTypeGroup";
+	String featureConfiguration = "featureConfiguration";
 	String FeatureConfiguration_districtName = "FeatureConfiguration.districtName";
 	String FeatureConfiguration_enabled = "FeatureConfiguration.enabled";
 	String FeatureConfiguration_endDate = "FeatureConfiguration.endDate";
@@ -2691,6 +2692,7 @@ public interface Captions {
 	String Sample_pathogenTestCount = "Sample.pathogenTestCount";
 	String Sample_pathogenTestingRequested = "Sample.pathogenTestingRequested";
 	String Sample_pathogenTestResult = "Sample.pathogenTestResult";
+	String Sample_performedByReferenceLaboratory = "Sample.performedByReferenceLaboratory";
 	String Sample_received = "Sample.received";
 	String Sample_receivedDate = "Sample.receivedDate";
 	String Sample_referredToUuid = "Sample.referredToUuid";
@@ -2704,6 +2706,7 @@ public interface Captions {
 	String Sample_requestedOtherPathogenTests = "Sample.requestedOtherPathogenTests";
 	String Sample_requestedPathogenTests = "Sample.requestedPathogenTests";
 	String Sample_requestedPathogenTestsTags = "Sample.requestedPathogenTestsTags";
+	String Sample_retestRequested = "Sample.retestRequested";
 	String Sample_sampleCode = "Sample.sampleCode";
 	String Sample_sampleDateTime = "Sample.sampleDateTime";
 	String Sample_sampleMaterial = "Sample.sampleMaterial";
@@ -3628,6 +3631,8 @@ public interface Captions {
 	String View_configuration_emailTemplates_short = "View.configuration.emailTemplates.short";
 	String View_configuration_facilities = "View.configuration.facilities";
 	String View_configuration_facilities_short = "View.configuration.facilities.short";
+	String View_configuration_featureConfiguration = "View.configuration.featureConfiguration";
+	String View_configuration_featureConfiguration_short = "View.configuration.featureConfiguration.short";
 	String View_configuration_laboratories = "View.configuration.laboratories";
 	String View_configuration_laboratories_short = "View.configuration.laboratories.short";
 	String View_configuration_linelisting = "View.configuration.linelisting";

sormas-api/src/main/java/de/symeda/sormas/api/i18n/Strings.java

@@ -702,6 +702,7 @@ public interface Strings {
 	String headingExternalMessagesDeleted = "headingExternalMessagesDeleted";
 	String headingExternalMessagesNotDeleted = "headingExternalMessagesNotDeleted";
 	String headingFatalities = "headingFatalities";
+	String headingFeatureConfiguration = "headingFeatureConfiguration";
 	String headingFetchExternalMessages = "headingFetchExternalMessages";
 	String headingFileExists = "headingFileExists";
 	String headingFilters = "headingFilters";
@@ -1069,6 +1070,7 @@ public interface Strings {
 	String infoExternalMessageHospitalizationMissingHospital = "infoExternalMessageHospitalizationMissingHospital";
 	String infoFacilityCsvImport = "infoFacilityCsvImport";
 	String infoFacilityNeedsDistrict = "infoFacilityNeedsDistrict";
+	String infoFeatureConfiguration = "infoFeatureConfiguration";
 	String infoHeadingAefiDashboardMap = "infoHeadingAefiDashboardMap";
 	String infoHeadingEnvironmentSampleDashboardMap = "infoHeadingEnvironmentSampleDashboardMap";
 	String infoHeadingSampleDashboardMap = "infoHeadingSampleDashboardMap";
@@ -1510,6 +1512,7 @@ public interface Strings {
 	String messageFacilityDearchived = "messageFacilityDearchived";
 	String messageFacilityDearchivingNotPossible = "messageFacilityDearchivingNotPossible";
 	String messageFacilityMulitChanged = "messageFacilityMulitChanged";
+	String messageFeatureConfigurationSaved = "messageFeatureConfigurationSaved";
 	String messageFollowUpCanceled = "messageFollowUpCanceled";
 	String messageFollowUpStatusChanged = "messageFollowUpStatusChanged";
 	String messageForwardedExternalMessageFound = "messageForwardedExternalMessageFound";

sormas-api/src/main/java/de/symeda/sormas/api/sample/SampleDto.java

@@ -78,6 +78,8 @@ public class SampleDto extends SormasToSormasShareableDto implements IsSample {
 	public static final String SAMPLING_REASON_DETAILS = "samplingReasonDetails";
 	public static final String DELETION_REASON = "deletionReason";
 	public static final String OTHER_DELETION_REASON = "otherDeletionReason";
+	public static final String PERFORMED_BY_REFERENCE_LABORATORY = "performedByReferenceLaboratory";
+	public static final String RETEST_REQUESTED = "retestRequested";
 
 	private CaseReferenceDto associatedCase;
 	private ContactReferenceDto associatedContact;
@@ -135,6 +137,8 @@ public class SampleDto extends SormasToSormasShareableDto implements IsSample {
 
 	private Boolean pathogenTestingRequested;
 	private Boolean additionalTestingRequested;
+	private Boolean performedByReferenceLaboratory;
+	private Boolean retestRequested = Boolean.FALSE;
 	private Set<PathogenTestType> requestedPathogenTests;
 	private Set<AdditionalTestType> requestedAdditionalTests;
 	@Size(max = FieldConstraints.CHARACTER_LIMIT_DEFAULT, message = Validations.textTooLong)
@@ -368,6 +372,22 @@ public void setAdditionalTestingRequested(Boolean additionalTestingRequested) {
 		this.additionalTestingRequested = additionalTestingRequested;
 	}
 
+	public Boolean getPerformedByReferenceLaboratory() {
+		return performedByReferenceLaboratory;
+	}
+
+	public void setPerformedByReferenceLaboratory(Boolean performedByReferenceLaboratory) {
+		this.performedByReferenceLaboratory = performedByReferenceLaboratory;
+	}
+
+	public Boolean getRetestRequested() {
+		return retestRequested;
+	}
+
+	public void setRetestRequested(Boolean retestRequested) {
+		this.retestRequested = retestRequested;
+	}
+
 	@ImportIgnore
 	public Set<PathogenTestType> getRequestedPathogenTests() {
 		return requestedPathogenTests;
@@ -489,6 +509,8 @@ private static void migrateAttributesOfPhysicalSample(SampleDto source, SampleDt
 		target.setSampleSource(source.getSampleSource());
 		target.setPathogenTestingRequested(source.getPathogenTestingRequested());
 		target.setAdditionalTestingRequested(source.getAdditionalTestingRequested());
+		target.setPerformedByReferenceLaboratory(source.getPerformedByReferenceLaboratory());
+		target.setRetestRequested(source.getRetestRequested());
 		target.setRequestedPathogenTests(source.getRequestedPathogenTests());
 		target.setRequestedAdditionalTests(source.getRequestedAdditionalTests());
 		target.setFieldSampleID(source.getFieldSampleID());

sormas-api/src/main/java/de/symeda/sormas/api/sample/SampleExportDto.java

@@ -89,6 +89,8 @@ public class SampleExportDto extends AbstractUuidDto implements IsSample {
 	private Boolean additionalTestingRequested;
 	private Set<AdditionalTestType> requestedAdditionalTests;
 	private String requestedOtherAdditionalTests;
+	private Boolean performedByReferenceLaboratory;
+	private Boolean retestRequested;
 	private boolean shipped;
 	private Date shipmentDate;
 	@SensitiveData
@@ -159,6 +161,7 @@ public SampleExportDto(long id, String uuid, String labSampleId, Date sampleRepo
 						   String contactRegion, String contactDistrict, String contactCommunity, String contactCaseRegion, String contactCaseDistrict, String contactCaseCommunity,
 						   Date contactReportDate, Date lastContactDate, ContactClassification contactClassification, ContactStatus contactStatus, String eventParticipantRegion, String eventParticipantDistrict,
                            String labUuid, String caseHealthFacilityUuid, String caseResponsibleRegion, String caseResponsibleDistrict, String caseResponsibleCommunity,
+						   Boolean performedByReferenceLaboratory, Boolean retestRequested,
 						   boolean isInJurisdiction, boolean isCaseInJurisdiction, boolean isContactInJurisdiction,  boolean isContactCaseInJurisdiction, boolean isEventParticipantInJurisdiction) {
 	//@formatter:on
 		super(uuid);
@@ -231,6 +234,8 @@ public SampleExportDto(long id, String uuid, String labSampleId, Date sampleRepo
 			}
 		}
 		this.requestedOtherAdditionalTests = requestedOtherAdditionalTests;
+		this.performedByReferenceLaboratory = performedByReferenceLaboratory;
+		this.retestRequested = retestRequested;
 		this.shipped = shipped;
 		this.shipmentDate = shipmentDate;
 		this.shipmentDetails = shipmentDetails;
@@ -858,6 +863,24 @@ public String getSampleMaterialSnomedCode() {
 		return material != null ? material.getSnomedCode() : null;
 	}
 
+	@Order(105)
+	public Boolean getPerformedByReferenceLaboratory() {
+		return performedByReferenceLaboratory;
+	}
+
+	public void setPerformedByReferenceLaboratory(Boolean performedByReferenceLaboratory) {
+		this.performedByReferenceLaboratory = performedByReferenceLaboratory;
+	}
+
+	@Order(106)
+	public Boolean getRetestRequested() {
+		return retestRequested;
+	}
+
+	public void setRetestRequested(Boolean retestRequested) {
+		this.retestRequested = retestRequested;
+	}
+
 	public SampleExportPathogenTest getPathogenTest1() {
 		return pathogenTest1;
 	}

sormas-api/src/main/resources/captions.properties

@@ -31,6 +31,7 @@ epiWeekFrom=From Epi Week
 epiWeekTo=To Epi Week
 facilityType=Facility type
 facilityTypeGroup=Facility category
+featureConfiguration=Feature Configuration
 firstName=First name
 sex=Sex
 nationalHealthId=National health ID
@@ -2285,6 +2286,7 @@ Sample.otherLab=Referral laboratory
 Sample.pathogenTestingRequested=Request pathogen tests to be performed?
 Sample.pathogenTestCount=Number of tests
 Sample.pathogenTestResult=Final laboratory result
+Sample.performedByReferenceLaboratory=Performed by reference laboratory
 Sample.received=Received
 Sample.receivedDate=Date sample received at lab
 Sample.referredToUuid=Sample referred to
@@ -2297,6 +2299,7 @@ Sample.requestedOtherAdditionalTests=Other requested additional tests
 Sample.requestedOtherPathogenTests=Other requested pathogen tests
 Sample.requestedPathogenTests=If you wish to request specific additional tests, tick each of them in the list below
 Sample.requestedPathogenTestsTags=Requested pathogen tests:
+Sample.retestRequested=Retest requested
 Sample.sampleCode=Sample code
 Sample.sampleDateTime=Date sample was collected
 Sample.sampleMaterial=Type of sample
@@ -3360,6 +3363,8 @@ View.configuration.documentTemplates=Document Templates Management
 View.configuration.documentTemplates.short=Document Templates
 View.configuration.facilities=Facilities Configuration
 View.configuration.facilities.short=Facilities
+View.configuration.featureConfiguration=Feature Configuration
+View.configuration.featureConfiguration.short=Features
 View.configuration.laboratories=Laboratories Configuration
 View.configuration.laboratories.short=Laboratories
 View.configuration.pointsofentry=Points of Entry Configuration

sormas-api/src/main/resources/enum.properties

@@ -872,6 +872,10 @@ FacilityType.CARE_RECIPIENT_HABITATION = Care recipient habitation
 FacilityType.VISITING_AMBULATORY_AID = Visiting ambulatory aid
 FacilityType.AFTER_SCHOOL = After school facility
 
+#FeatureType
+FeatureType.SAMPLE_ADD_PATHOGEN_TEST=Allow adding pathogen tests from a sample
+FeatureType.PATHOGEN_TEST_RESULT_REQUIRED=Require a result when entering a pathogen test
+
 #FacilityTypeGroup
 FacilityTypeGroup.ACCOMMODATION=Accommodation
 FacilityTypeGroup.CARE_FACILITY=Care facility

sormas-api/src/main/resources/strings.properties

@@ -609,6 +609,7 @@ headingEventsNotDeleted = None of the events were deleted
 headingEventsNotRestored = None of the events were restored
 headingExportFailed = Export failed
 headingFatalities=Fatalities
+headingFeatureConfiguration = Feature Configuration
 headingFileExists = Duplicate File
 headingFilters = Filters
 headingStoppedFollowUp = Stopped Follow-up
@@ -1016,6 +1017,7 @@ infoExpectedFollowUpUntilDateContact = The expected follow-up until date for thi
 infoExportNoFilters = <b>Warning:</b> No filters have been selected. Export may take a while.
 infoFacilityCsvImport = Name of a configured facility (requires FacilityType), OTHER_FACILITY (requires FacilityType and FacilityDetails) or NO_FACILITY
 infoFacilityNeedsDistrict = Please define a district in order to select a facility.
+infoFeatureConfiguration = Enable or disable optional system features. Changes take effect immediately and apply to the whole server.
 infoImmunizationPeriod = Immunization period of this immunization
 infoImmunizationStatusAcquired = Only immunizations with acquired status are considered
 infoImmunizationValidFromClosest = Selects the immunization with the valid from date closest to (but not after) the case report date
@@ -1361,6 +1363,7 @@ messageCountEventsNotDeletedSormasToSormasReason = %s events not deleted because
 messageExportFailed = There was an error preventing the data to be exported. Please contact an admin and inform them about this issue.
 messageExportConfigurationDeleted = Export configuration deleted
 messageExportConfigurationSaved = Export configuration saved
+messageFeatureConfigurationSaved = Feature configuration saved
 messageFollowUpCanceled = Follow-up of all selected contacts has been canceled
 messageFollowUpStatusChanged = Follow-up of all selected contacts that have follow-up has been set to lost to follow-up
 messageFacilityChanged = You have changed the facility of this case. Do you want to transfer the case to the new facility (the hospitalization may be updated) or do you only want to edit the data to correct a mistake?

sormas-backend/src/main/java/de/symeda/sormas/backend/feature/FeatureConfigurationFacadeEjb.java

@@ -346,6 +346,26 @@ public void saveFeatureConfiguration(@Valid FeatureConfigurationIndexDto configu
 		service.ensurePersisted(entity);
 	}
 
+	@Override
+	public void setServerFeatureEnabled(FeatureType featureType, boolean enabled) {
+
+		if (!featureType.isServerFeature()) {
+			throw new IllegalArgumentException("FeatureType " + featureType + " is not a server feature and cannot be toggled here.");
+		}
+
+		List<FeatureConfiguration> configurations = service.getServerFeatureConfigurationsByType(featureType);
+		if (configurations.isEmpty()) {
+			FeatureConfiguration configuration = FeatureConfiguration.build(featureType, enabled);
+			configuration.setProperties(featureType.getSupportedPropertyDefaults());
+			service.ensurePersisted(configuration);
+		} else {
+			for (FeatureConfiguration configuration : configurations) {
+				configuration.setEnabled(enabled);
+				service.ensurePersisted(configuration);
+			}
+		}
+	}
+
 	@Override
 	public void deleteAllFeatureConfigurations(FeatureConfigurationCriteria criteria) {
 

sormas-backend/src/main/java/de/symeda/sormas/backend/feature/FeatureConfigurationService.java

@@ -1,5 +1,6 @@
 package de.symeda.sormas.backend.feature;
 
+import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Date;
 import java.util.HashMap;
@@ -16,6 +17,7 @@
 import javax.persistence.criteria.From;
 import javax.persistence.criteria.JoinType;
 import javax.persistence.criteria.Predicate;
+import javax.persistence.criteria.Root;
 
 import org.apache.commons.collections4.MapUtils;
 import org.apache.commons.lang3.ArrayUtils;
@@ -201,6 +203,21 @@ private Map<FeatureType, FeatureConfiguration> getServerFeatureConfigurations()
 			.collect(Collectors.toMap(FeatureConfiguration::getFeatureType, Function.identity(), (e1, e2) -> e2));
 	}
 
+	public FeatureConfiguration getServerFeatureConfiguration(FeatureType featureType) {
+		return getServerFeatureConfigurations().get(featureType);
+	}
+
+	public List<FeatureConfiguration> getServerFeatureConfigurationsByType(FeatureType featureType) {
+		if (!featureType.isServerFeature()) {
+			return new ArrayList<>();
+		}
+		CriteriaBuilder cb = em.getCriteriaBuilder();
+		CriteriaQuery<FeatureConfiguration> cq = cb.createQuery(FeatureConfiguration.class);
+		Root<FeatureConfiguration> root = cq.from(FeatureConfiguration.class);
+		cq.where(cb.equal(root.get(FeatureConfiguration.FEATURE_TYPE), featureType));
+		return em.createQuery(cq).getResultList();
+	}
+
 	private boolean hasEnabledDependentFeature(FeatureType featureType, Map<FeatureType, FeatureConfiguration> featureConfigurationMap) {
 
 		for (FeatureType dependentFeatureType : featureType.getDependentFeatures()) {

sormas-backend/src/main/java/de/symeda/sormas/backend/sample/PathogenTestFacadeEjb.java

@@ -45,6 +45,7 @@
 import de.symeda.sormas.api.common.DeletionDetails;
 import de.symeda.sormas.api.common.Page;
 import de.symeda.sormas.api.environment.environmentsample.EnvironmentSampleReferenceDto;
+import de.symeda.sormas.api.feature.FeatureType;
 import de.symeda.sormas.api.i18n.I18nProperties;
 import de.symeda.sormas.api.i18n.Validations;
 import de.symeda.sormas.api.sample.PathogenTestCriteria;
@@ -78,6 +79,7 @@
 import de.symeda.sormas.backend.event.EventFacadeEjb.EventFacadeEjbLocal;
 import de.symeda.sormas.backend.event.EventParticipant;
 import de.symeda.sormas.backend.event.EventParticipantFacadeEjb.EventParticipantFacadeEjbLocal;
+import de.symeda.sormas.backend.feature.FeatureConfigurationFacadeEjb.FeatureConfigurationFacadeEjbLocal;
 import de.symeda.sormas.backend.infrastructure.country.CountryFacadeEjb;
 import de.symeda.sormas.backend.infrastructure.country.CountryService;
 import de.symeda.sormas.backend.infrastructure.facility.FacilityFacadeEjb;
@@ -132,6 +134,8 @@ public class PathogenTestFacadeEjb implements PathogenTestFacade {
 	private ConfigFacadeEjbLocal configFacade;
 	@EJB
 	private DrugSusceptibilityMapper drugSusceptibilityMapper;
+	@EJB
+	private FeatureConfigurationFacadeEjbLocal featureConfigurationFacade;
 
 	@Override
 	public List<String> getAllActiveUuids() {
@@ -435,6 +439,13 @@ public PathogenTestDto savePathogenTest(@Valid PathogenTestDto dto, boolean chec
 
 		restorePseudonymizedDto(dto, existingSampleTest, existingSampleTestDto);
 
+		// When the administrator has not made the result mandatory (#13948 issue #13958), an empty result is
+		// allowed; default it to PENDING so the non-null DB constraint holds. This covers every save path
+		// (UI, environment samples, external-message processing, REST), not just the human-sample UI flow.
+		if (dto.getTestResult() == null && !featureConfigurationFacade.isFeatureEnabled(FeatureType.PATHOGEN_TEST_RESULT_REQUIRED)) {
+			dto.setTestResult(PathogenTestResultType.PENDING);
+		}
+
 		validate(dto);
 
 		PathogenTest pathogenTest = fillOrBuildEntity(dto, existingSampleTest, checkChangeDate);